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core::select::residue_selector::SecondaryStructureSelector Class Reference

#include <SecondaryStructureSelector.hh>

Inheritance diagram for core::select::residue_selector::SecondaryStructureSelector:
Inheritance graph
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Public Member Functions

 SecondaryStructureSelector ()
 
 SecondaryStructureSelector (std::string const &selected)
 
ResidueSelectorOP clone () const override
 Clone operator. More...
 
 ~SecondaryStructureSelector () override
 
ResidueSubset apply (core::pose::Pose const &pose) const override
 Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
 Initialize any data members of this instance from an input tag and a DataMap object. More...
 
std::string get_name () const override
 
void set_overlap (core::Size const overlapval)
 sets number of residues around the given SS elements to select (default=0) More...
 
void set_minH (core::Size const minHval)
 sets the minimal number of consecutive H residues to keep the secondary structure assignation (default=1) More...
 
void set_minE (core::Size const minEval)
 sets the minimal number of consecutive E residues to keep the secondary structure assignation (default=1) More...
 
void set_selected_ss (std::string const &selected)
 sets ss characters to select – must be set prior to apply() More...
 
void set_include_terminal_loops (bool const inc_term)
 if true, one-residue terminal "loops" will be included (default=false) More...
 
void set_pose_secstruct (std::string const &ss)
 Override pose secondary structure. The secondary structure set by this method will always be used if it is non-empty. More...
 
void set_use_dssp (bool const use_dssp)
 If set, dssp will be used to determine secondary structure. Has no effect if pose_secstruct_ is set. More...
 
- Public Member Functions inherited from core::select::residue_selector::ResidueSelector
 ResidueSelector ()
 Constructor. More...
 
 ~ResidueSelector () override
 Destructor. More...
 
virtual bool residue_selector_provides_citation_info () const
 Does this residue selector provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool residue_selector_is_unpublished () const
 Does this residue selector indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Member Functions

std::string get_secstruct (core::pose::Pose const &pose) const
 gets the secondary structure to be used by the selector More...
 
void fix_secstruct_definition (std::string &ss) const
 fixes the secondary structure according to the expected minimal length of each secondary structure. More...
 
void add_overlap (ResidueSubset &matching_ss, pose::Pose const &pose, std::string const &ss) const
 
bool check_ss (std::string const &ss) const
 

Private Attributes

std::string pose_secstruct_
 
core::Size overlap_
 
core::Size minH_
 
core::Size minE_
 
bool include_terminal_loops_
 
bool use_dssp_
 
std::set< char > selected_ss_
 

Constructor & Destructor Documentation

core::select::residue_selector::SecondaryStructureSelector::SecondaryStructureSelector ( )

References selected_ss_.

core::select::residue_selector::SecondaryStructureSelector::SecondaryStructureSelector ( std::string const &  selected)

References check_ss(), and set_selected_ss().

core::select::residue_selector::SecondaryStructureSelector::~SecondaryStructureSelector ( )
overridedefault

Member Function Documentation

void core::select::residue_selector::SecondaryStructureSelector::add_overlap ( ResidueSubset matching_ss,
pose::Pose const &  pose,
std::string const &  ss 
) const
private
ResidueSubset core::select::residue_selector::SecondaryStructureSelector::apply ( core::pose::Pose const &  pose) const
overridevirtual

Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not.

Implements core::select::residue_selector::ResidueSelector.

References add_overlap(), check_ss(), fix_secstruct_definition(), get_secstruct(), selected_ss_, core::pose::Pose::size(), and core::select::residue_selector::TR().

Referenced by protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::apply().

bool core::select::residue_selector::SecondaryStructureSelector::check_ss ( std::string const &  ss) const
private
std::string core::select::residue_selector::SecondaryStructureSelector::class_name ( )
static
ResidueSelectorOP core::select::residue_selector::SecondaryStructureSelector::clone ( ) const
overridevirtual

Clone operator.

Copy this object and return an owning pointer to the new object.

Implements core::select::residue_selector::ResidueSelector.

void core::select::residue_selector::SecondaryStructureSelector::fix_secstruct_definition ( std::string &  ss) const
private

fixes the secondary structure according to the expected minimal length of each secondary structure.

Parameters
[in]ssstring with the secondary structure definition

References core::pack::dunbrack::c, minE_, minH_, and core::select::residue_selector::TR().

Referenced by apply().

std::string core::select::residue_selector::SecondaryStructureSelector::get_name ( ) const
overridevirtual
std::string core::select::residue_selector::SecondaryStructureSelector::get_secstruct ( core::pose::Pose const &  pose) const
private

gets the secondary structure to be used by the selector

Parameters
[in]poseInput pose

Determines secondary structure by the following rules:

  1. If pose_secstruct_ is user-specified, use that
  2. If use_dssp_ is true, run DSSP and use DSSP secstruct
  3. If use_dssp_ is false, return pose.secstruct()

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::get_dssp_secstruct(), pose_secstruct_, core::pose::Pose::secstruct(), core::select::residue_selector::TR(), and use_dssp_.

Referenced by apply().

void core::select::residue_selector::SecondaryStructureSelector::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datacache 
)
overridevirtual

Initialize any data members of this instance from an input tag and a DataMap object.

Noop implementation in the base class in the case that a derived class has no need to read data from an input tag

Reimplemented from core::select::residue_selector::ResidueSelector.

References check_ss(), include_terminal_loops_, minE_, minH_, overlap_, pose_secstruct_, set_include_terminal_loops(), set_minE(), set_minH(), set_overlap(), set_pose_secstruct(), set_selected_ss(), set_use_dssp(), and use_dssp_.

void core::select::residue_selector::SecondaryStructureSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::select::residue_selector::SecondaryStructureSelector::set_include_terminal_loops ( bool const  inc_term)

if true, one-residue terminal "loops" will be included (default=false)

References include_terminal_loops_.

Referenced by parse_my_tag().

void core::select::residue_selector::SecondaryStructureSelector::set_minE ( core::Size const  minEval)

sets the minimal number of consecutive E residues to keep the secondary structure assignation (default=1)

References minE_.

Referenced by protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::apply(), and parse_my_tag().

void core::select::residue_selector::SecondaryStructureSelector::set_minH ( core::Size const  minHval)

sets the minimal number of consecutive H residues to keep the secondary structure assignation (default=1)

References minH_.

Referenced by parse_my_tag().

void core::select::residue_selector::SecondaryStructureSelector::set_overlap ( core::Size const  overlapval)

sets number of residues around the given SS elements to select (default=0)

References overlap_.

Referenced by parse_my_tag().

void core::select::residue_selector::SecondaryStructureSelector::set_pose_secstruct ( std::string const &  ss)

Override pose secondary structure. The secondary structure set by this method will always be used if it is non-empty.

References pose_secstruct_.

Referenced by parse_my_tag().

void core::select::residue_selector::SecondaryStructureSelector::set_selected_ss ( std::string const &  selected)

sets ss characters to select – must be set prior to apply()

References selected_ss_.

Referenced by parse_my_tag(), and SecondaryStructureSelector().

void core::select::residue_selector::SecondaryStructureSelector::set_use_dssp ( bool const  use_dssp)

If set, dssp will be used to determine secondary structure. Has no effect if pose_secstruct_ is set.

Determines secondary structure by the following rules:

  1. If pose_secstruct_ is user-specified, use that
  2. If use_dssp_ is true, run DSSP and use DSSP secstruct
  3. If use_dssp_ is false, return pose.secstruct()

References use_dssp_.

Referenced by parse_my_tag().

Member Data Documentation

bool core::select::residue_selector::SecondaryStructureSelector::include_terminal_loops_
private
core::Size core::select::residue_selector::SecondaryStructureSelector::minE_
private
core::Size core::select::residue_selector::SecondaryStructureSelector::minH_
private
core::Size core::select::residue_selector::SecondaryStructureSelector::overlap_
private
std::string core::select::residue_selector::SecondaryStructureSelector::pose_secstruct_
private
std::set< char > core::select::residue_selector::SecondaryStructureSelector::selected_ss_
private
bool core::select::residue_selector::SecondaryStructureSelector::use_dssp_
private

The documentation for this class was generated from the following files: